Intelligence papers on a reported UFO sighting known as the "Rendlesham incident" have gone missing, files from the National Archives reveal.
The missing files relate to a report of mysterious lights from US servicemen at RAF Woodbridge in Suffolk in 1980.
The disappearance came to light with the release of 8,000 previously classified documents on UFOs.
Officials found a "huge" gap where defence intelligence files relating to the case should be, the papers show.
The documents are the latest MoD files on UFOs released into the National Archives which will be free to access on its website for a month.
Photographs and sketches of UFOs made by members of the public are included, as well as their eyewitness reports.
Among the documents is testimony from an airline pilot and his son who say they spent five minutes watching an object made up of three circles fly past their garden in Hellingly, East Sussex.
The pilot reported it to Air Traffic Control in West Drayton, and an official labelled his sighting as one by "a credible witness".
But another defence official later wrote a memo saying the report "contains nothing of air defence significance".
More attention is given to the crew of an RAF Tornado who encountered an object the size of a C130 Hercules transport aircraft while flying over the North Sea in 1990.
The pilot describes flying at Mach 0.8 but being overtaken by an aircraft the like of which he had never seen before.
He talks about lights and even "an engine area" but the files also show how a possible explanation emerges - a Russian rocket booster was re-entering the earth's atmosphere on that same night.
Another file released reveals six small "flying saucers" were found by members of the public in locations across southern England in 1967. Four police forces and the army were mobilised before it emerged the incident was a rag-day hoax by engineering students from Farnborough Technical College.
There is also a report from a London man who believed he may have been abducted by aliens.
The files reveal that key documentation relating to the Rendlesham Forest incident has disappeared.
Some UFO researchers believe the episode, which happened over two nights in 1980 is a classic example of a "close encounter".
The incident took place near the fence of RAF Woodbridge - at that time being used by the US Air Force. A group of servicemen reported seeing strange lights in the trees near the base and after investigating found marks on the ground and damage to vegetation.
The files reveal the MoD received a request for its own records of the incident in 2000, but when officials looked they discovered a "huge" gap where defence intelligence files relating to it should be.
The hunt generated a series of notes, with one official speculating that the files could have been taken home by someone and another remarking that "it could be interpreted to mean that a deliberate attempt had been made to eradicate the records covering this incident".
However, among intelligence papers released in 2009, it was revealed that former Admiral of the Fleet Lord Hill-Norton wrote to the defence secretary about the incident in 1985, speculating that an unauthorised aircraft may have entered and left UK airspace at the time.
But it is not the only gap in the official record. In 2002 the MoD received a request for information from Lord Hill-Norton. He wanted to know about reports of a UFO sighting made by HMS Manchester while on exercise in the 1990s.
It emerged in the file that HMS Manchester's log for one of the periods was lost overboard after "a gust of wind" and the vessel's captain cannot remember anything unusual taking place.
This latest tranche of documents covers not just people who contacted the Ministry of Defence after seeing lights or objects, but also sheds some light on official thinking about this aspect of the paranormal.
Concern about UFOs and what they might be went up to senior level and lasted several years.
Officials were dismayed when in 1977 the then Prime Minister of Grenada Sir Eric Gairy wanted to call for the United Nations to set up a unit to investigate the phenomenon.
The files show how Britain was concerned the idea would drag the UN into disrepute. The premier was persuaded to withdraw his proposal but went on to call for 1978 to be designated "the year of the UFO". He was deposed in a coup the following year.
UFOs have only ever received one debate in Parliament. It came in the House of Lords in 1979, at the height of the "winter of discontent", and the files show how officials laboured to prepare a government position on the topic.
At the end of the discussion the government spokesman Lord Stabolgi summed up what remains the official position now.
"There is nothing to convince Her Majesty's government that there has ever been a single visit by an alien spacecraft. As for telling the public the truth about UFOs, the truth is simple.
"There really are many strange phenomena in the sky, and these are invariably reported by rational people. But there is a wide range of natural explanations to account for such phenomena."